beadarraySNP 1.39.0
Jan Oosting
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarraySNP | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.39.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarraySNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘beadarraySNP’ version ‘1.39.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘beadarraySNP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘DNAcopy’ ‘aCGH’ ‘affy’ ‘beadarray’ ‘limma’ ‘snapCGH’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
IlluminaGetGencalls: no visible global function definition for
‘read.table’
IlluminaGetOPAinfo: no visible global function definition for
‘read.table’
Sample_Map2Samplesheet: no visible global function definition for
‘read.table’
Sample_Map2Samplesheet: no visible global function definition for
‘write.table’
backgroundCorrect.SNP : delta.vec: no visible global function
definition for ‘quantile’
backgroundCorrect.SNP: no visible global function definition for
‘normexp.fit’
backgroundCorrect.SNP: no visible global function definition for
‘normexp.signal’
backgroundCorrect.SNP: no visible binding for global variable
‘bg.adjust’
backgroundEstimate : intminBG: no visible global function definition
for ‘lm’
backgroundEstimate: no visible global function definition for ‘density’
calculateLair: no visible global function definition for ‘quantile’
calculateQCarray: no visible global function definition for ‘median’
convert2aCGH: no visible global function definition for ‘create.aCGH’
createCNSummary: no visible global function definition for ‘aggregate’
dist.GT: no visible global function definition for ‘as.dist’
heterozygousSNPs: no visible binding for global variable ‘quantile’
interactiveCNselect: no visible global function definition for
‘locator’
interactiveCNselect: no visible global function definition for ‘text’
normalizeBetweenAlleles.SNP: no visible global function definition for
‘normalizeQuantiles’
normalizeBetweenSubsamples.SNP: no visible global function definition
for ‘normalizeQuantiles’
normalizeLoci.SNP: no visible binding for global variable ‘median’
normalizeLoci.SNP: no visible global function definition for ‘coef’
normalizeLoci.SNP: no visible global function definition for ‘lm’
normalizeWithinArrays.SNP: no visible global function definition for
‘quantile’
pdfChromosomeGainLossLOH: no visible global function definition for
‘pdf’
pdfChromosomeGainLossLOH: no visible global function definition for
‘par’
pdfChromosomeGainLossLOH: no visible global function definition for
‘dev.off’
pdfChromosomesSmoothCopyNumber: no visible global function definition
for ‘pdf’
pdfChromosomesSmoothCopyNumber: no visible global function definition
for ‘par’
pdfChromosomesSmoothCopyNumber: no visible global function definition
for ‘dev.off’
pdfQC : reportSingleObject: no visible global function definition for
‘par’
pdfQC : reportSingleObject: no visible global function definition for
‘mtext’
pdfQC: no visible global function definition for ‘pdf’
pdfQC: no visible global function definition for ‘dev.off’
pdfSamplesSmoothCopyNumber: no visible global function definition for
‘pdf’
pdfSamplesSmoothCopyNumber: no visible global function definition for
‘dev.off’
plotGenomePanels: no visible global function definition for ‘par’
plotGenomePanels: no visible global function definition for ‘plot’
plotGenomePanels: no visible global function definition for ‘abline’
plotGenomePanels: no visible global function definition for ‘points’
plotGenomePanels: no visible global function definition for ‘text’
plotGenomePanels: no visible global function definition for ‘axis’
plotGenomePanels: no visible global function definition for ‘segments’
plotGenomePanels: no visible global function definition for ‘rect’
plotGoldenGate4OPA: no visible global function definition for ‘par’
plotGoldenGate4OPA: no visible global function definition for ‘plot’
plotGoldenGate4OPA: no visible global function definition for ‘abline’
plotGoldenGate4OPA: no visible global function definition for ‘points’
plotGoldenGate4OPA: no visible global function definition for ‘text’
plotGoldenGate4OPA: no visible global function definition for ‘axis’
plotGoldenGate4OPA: no visible global function definition for
‘segments’
plotGoldenGate4OPA: no visible global function definition for ‘rect’
plotGroupZygosity: no visible global function definition for ‘plot’
plotGroupZygosity: no visible global function definition for ‘points’
read.SnpSetIllumina: no visible global function definition for
‘read.table’
read.SnpSetIllumina: no visible global function definition for
‘readIllumina’
read.SnpSetIllumina: no visible global function definition for
‘summarize’
read.SnpSetIllumina: no visible global function definition for
‘aggregate’
read.SnpSetIllumina: no visible binding for global variable ‘median’
read.SnpSetIllumina: no visible binding for global variable ‘sd’
read.SnpSetIllumina: no visible global function definition for
‘type.convert’
readReportfile: no visible global function definition for ‘read.table’
removeLowQualityProbes: no visible global function definition for
‘median’
removeLowQualityProbes: no visible binding for global variable ‘median’
removeLowQualitySamples: no visible binding for global variable
‘median’
reportChromosomeGainLossLOH: no visible global function definition for
‘plot’
reportChromosomeGainLossLOH: no visible global function definition for
‘par’
reportChromosomeGainLossLOH: no visible global function definition for
‘rect’
reportChromosomeGainLossLOH: no visible global function definition for
‘axis’
reportChromosomeGainLossLOH: no visible global function definition for
‘abline’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘par’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘plot’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘legend’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘abline’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘rect’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘points’
reportChromosomesSmoothCopyNumber: no visible global function
definition for ‘lines’
reportGenomeGainLossLOH: no visible global function definition for
‘plot’
reportGenomeGainLossLOH: no visible global function definition for
‘par’
reportGenomeGainLossLOH: no visible global function definition for
‘rect’
reportGenomeGainLossLOH: no visible global function definition for
‘abline’
reportGenomeGainLossLOH: no visible global function definition for
‘axis’
reportGenomeIntensityPlot: no visible global function definition for
‘aggregate’
reportGenomeIntensityPlot: no visible global function definition for
‘plot’
reportGenomeIntensityPlot: no visible global function definition for
‘par’
reportGenomeIntensityPlot: no visible global function definition for
‘abline’
reportGenomeIntensityPlot: no visible global function definition for
‘axis’
reportGenomeIntensityPlot: no visible global function definition for
‘points’
reportGenomeIntensityPlot: no visible global function definition for
‘segments’
reportGenomeIntensityPlot: no visible global function definition for
‘lines’
reportGenotypeSegmentation: no visible global function definition for
‘par’
reportGenotypeSegmentation: no visible global function definition for
‘plot’
reportGenotypeSegmentation: no visible global function definition for
‘points’
reportGenotypeSegmentation: no visible global function definition for
‘axis’
reportGenotypeSegmentation: no visible global function definition for
‘abline’
reportGenotypeSegmentation: no visible global function definition for
‘segments’
reportGroupZygosity: no visible global function definition for ‘pdf’
reportGroupZygosity: no visible global function definition for ‘par’
reportGroupZygosity: no visible global function definition for
‘dev.off’
reportSamplesSmoothCopyNumber: no visible global function definition
for ‘par’
reportSamplesSmoothCopyNumber: no visible global function definition
for ‘lines’
reportSamplesSmoothCopyNumber: no visible global function definition
for ‘rect’
reportSamplesSmoothCopyNumber: no visible global function definition
for ‘points’
reportSamplesSmoothCopyNumber: no visible global function definition
for ‘legend’
segmentate: no visible global function definition for ‘smooth.CNA’
segmentate: no visible global function definition for ‘CNA’
segmentate: no visible global function definition for ‘aggregate’
segmentate.old: no visible global function definition for ‘runDNAcopy’
segmentate.old: no visible global function definition for ‘runHomHMM’
segmentate.old: no visible global function definition for ‘runBioHMM’
segmentate.old: no visible global function definition for ‘runGLAD’
segmentate.old: no visible global function definition for ‘mergeStates’
plotQC,QCIllumina : image.plate: no visible global function definition
for ‘gray’
plotQC,QCIllumina : image.plate: no visible global function definition
for ‘image’
plotQC,QCIllumina : checkerboard: no visible global function definition
for ‘strwidth’
plotQC,QCIllumina : checkerboard: no visible global function definition
for ‘text’
plotQC,QCIllumina: no visible global function definition for ‘rgb’
reportSamplePanelQC,QCIllumina: no visible global function definition
for ‘rgb’
reportSamplePanelQC,QCIllumina: no visible global function definition
for ‘barplot’
reportSamplePanelQC,QCIllumina: no visible global function definition
for ‘plot’
Undefined global functions or variables:
CNA abline aggregate as.dist axis barplot bg.adjust coef create.aCGH
density dev.off gray image legend lines lm locator median mergeStates
mtext normalizeQuantiles normexp.fit normexp.signal par pdf plot
points quantile read.table readIllumina rect rgb runBioHMM runDNAcopy
runGLAD runHomHMM sd segments smooth.CNA strwidth summarize text
type.convert write.table
Consider adding
importFrom("grDevices", "dev.off", "gray", "pdf", "rgb")
importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
"lines", "locator", "mtext", "par", "plot", "points",
"rect", "segments", "strwidth", "text")
importFrom("stats", "aggregate", "as.dist", "coef", "density", "lm",
"median", "quantile", "sd")
importFrom("utils", "read.table", "type.convert", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/beadarraySNP.Rcheck/00check.log’
for details.